Polyadenylated RNA isolated from the archaebacterium Halobacterium halobium

Brown, Jamesw .; Reeve, John N.

doi:10.1128/jb.166.2.686-688.1986

Cited by 22 publications

(7 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Archaea are microscopic, single-celled organisms with no nucleus, no mitochondria and no chloroplasts. Regarding mRNA, they are more similar to bacteria than to eukaryotes: mRNA does not have introns, it is polycistronic, is not modified and does not have long stabilizing poly(A) tails at the 3 0 end (Brown & Coleman, 1975;Brown & Reeve, 1986). However, in Sulfolobus and Methanothermobacter, the existence of an archaeal exosome with characteristics of the eukaryotic exosome was demonstrated (Evguenieva-Hackenberg et al, 2003;Farhoud et al, 2005).…”

Section: Rna-degrading Machinesmentioning

confidence: 99%

The critical role of RNA processing and degradation in the control of gene expression

et al. 2010

View full text Add to dashboard Cite

The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.

show abstract

Section: Rna-degrading Machinesmentioning

confidence: 99%

The critical role of RNA processing and degradation in the control of gene expression

et al. 2010

View full text Add to dashboard Cite

show abstract

“…The coupling of transcription and translation in Archaea (7) suggests that mRNA degradation in the Archaea might be more closely related to processes in bacteria than in eukaryotes. To our knowledge, archaeal mRNA is not capped, nor have homologues of eukaryotic enzymes involved in mRNA capping, decapping, and 5Ј-to 3Ј-exoribonucleolytic degradation been identified in archaeal genomes (1,8,9). However, a eukaryotic-like exosome with a 3Ј-to 5Ј-exoribonucleolytic activity is present in most Archaea (10,11) with the exception of the halophilic archaeon Haloferax where this activity is carried out by RNase R (12).…”

mentioning

confidence: 99%

Euryarchaeal β-CASP Proteins with Homology to Bacterial RNase J Have 5′- to 3′-Exoribonuclease Activity

Clouet‐d’Orval

Rinaldi

Quentin

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

In the Archaea only a handful of ribonucleases involved in RNA processing and degradation have been characterized. One potential group of archaeal ribonucleases are homologues of the bacterial RNase J family, which have a ␤-CASP metallo-␤-lactamase fold. Here we show that ␤-CASP proteins encoded in the genomes of the hyperthermophilic Euryarchaeota Pyrococcus abyssi and Thermococcus kodakaraensis are processive exoribonucleases with a 5 end dependence and a 5 to 3 directionality. We named these enzymes Pab-RNase J and Tk-RNase J, respectively. RNAs with 5-monophosphate or 5-hydroxyl ends are preferred substrates of Pab-RNase J, whereas circularized RNA is resistant to Pab-RNase J activity. Degradation of a 3 endlabeled synthetic RNA in which an internal nucleoside is substituted by three ethylene glycol units generates intermediates demonstrating 5 to 3 directionality. The substitution of conserved residues in Pab-RNase J predicted to be involved in the coordination of metal ions demonstrates their importance for ribonuclease activity, although the detailed geometry of the catalytic site is likely to differ from bacterial RNase J. This is the first identification of a 5-exoribonuclease encoded in the genomes of the Archaea. Phylogenetic analysis shows that euryarchaeal RNase J has been inherited vertically, suggesting an ancient origin predating the separation of the Bacteria and the Archaea.The study of RNA metabolism in Archaea is in its infancy (for a recent review, see Ref. 1). The control of RNA processing and mRNA stability are important steps of gene expression. As in all domains of life, processing of tRNA in Archaea is performed by the ribonucleoprotein RNase P (2) and the endoribonuclease RNase Z (3, 4). The RNA-splicing endoribonuclease removes introns from archaeal pre-tRNA and participates in rRNA processing (5, 6). The coupling of transcription and translation in Archaea (7) suggests that mRNA degradation in the Archaea might be more closely related to processes in bacteria than in eukaryotes. To our knowledge, archaeal mRNA is not capped, nor have homologues of eukaryotic enzymes involved in mRNA capping, decapping, and 5Ј-to 3Ј-exoribonucleolytic degradation been identified in archaeal genomes (1, 8, 9). However, a eukaryotic-like exosome with a 3Ј-to 5Ј-exoribonucleolytic activity is present in most Archaea (10, 11) with the exception of the halophilic archaeon Haloferax where this activity is carried out by RNase R (12). Overall, our comprehension of mRNA degradation in Archaea is very limited, whereas it is quite advanced in Eukarya and bacteria.In bacteria as well as in Eukarya, the nature of the 5Ј end of mRNA is an important determinant for stability. In the model Gram-negative bacterium Escherichia coli, RNase E, a key enzyme in mRNA degradation, is a 5Ј end-dependent endoribonuclease (13,14). Indeed substrates with 5Ј-monophosphate ends stimulate RNase E activity (15-17). In the model Grampositive bacterium Bacillus subtilis, the recently identified and characterized RNase J was discovere...

show abstract

“…Archaeal mRNAs are not capped; some mRNAs were reported to carry short poly(A) tails (9,10,47). A number of RNases with functions in the processing and maturation of…”

mentioning

confidence: 99%

Global Analysis of mRNA Decay in Halobacterium salinarum NRC-1 at Single-Gene Resolution Using DNA Microarrays

et al. 2007

View full text Add to dashboard Cite

RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1,717 open reading frames, 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 min to more than 18 min, with 79% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min, which is considerably longer than the ones found in the other prokaryotes investigated thus far. As previously observed in Escherichia coli and Saccharomyces cerevisiae, we could not detect a significant correlation between transcript length and transcript stability, but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives. These results provide initial insights into mRNA turnover in a euryarchaeon. Moreover, our model organism, H. salinarum NRC-1, is one of just two archaea sequenced to date that are missing the core subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced thus far.Fast decay of mRNA allows quick adaptation of organisms to changes in the environment by altering the expression of selected genes. The half-lives of individual transcripts or even transcript segments within an organism show considerable variations contributing to differential gene expression. The stabilities of several bacterial transcripts vary in response to external factors (reviewed in reference 46); the stabilities of eukaryotic transcripts can vary in response to cellular stimuli and differentiation stage (reviewed, for example, in reference 42), thus contributing to regulated gene expression. Microarray technology allows the study of mRNA half-lives of organisms on a global level. Up to now such studies have been performed for the bacterial model organisms Escherichia coli (6, 45) and Bacillus subtilis (18) and the eukaryotic model organism Saccharomyces cerevisiae (49), as well as two species of the hyperthermophilic crenarchaeon Sulfolobus (2). In all of these organisms a wide range of stabilities was found for individual mRNAs. Most E. coli and B. subtilis mRNAs (80%) exhibited half-lives of 3 to 8 min (6, 18). A study of the effect of the Staphylococcus aureus virulence factor regulator SarA on logphase mRNA half-lives in this organism revealed that 90% of mRNAs expressed during log-phase growth had half-lives below 5 min (41). In the two Sulfolobus species the median half-life was found to be...

show abstract

Polyadenylated RNA isolated from the archaebacterium Halobacterium halobium

Cited by 22 publications

References 11 publications

The critical role of RNA processing and degradation in the control of gene expression

The critical role of RNA processing and degradation in the control of gene expression

Euryarchaeal β-CASP Proteins with Homology to Bacterial RNase J Have 5′- to 3′-Exoribonuclease Activity

Global Analysis of mRNA Decay in Halobacterium salinarum NRC-1 at Single-Gene Resolution Using DNA Microarrays

Contact Info

Product

Resources

About